As intended, laboratories used a wide variety of methods, including multiple LC-MS/MS instruments, MALDI-MS, and FT-ICR-MS; depletion of abundant proteins; fractionation of intact proteins on 2-D gels or with LC or IEF methods; protein enrichment or labeling methods; immunoassays or antibody arrays; and direct (SELDI) MS. They also varied on choice of search algorithm and database, and criteria for declaring high or lower confidence identification ofpeptide sequences and matching proteins (Tab. 1). In general, the numbers of proteins reported individually by the labs do not have the integration feature which was applied to the whole PPP dataset. In several cases, much more extensive analyses were reported. Thus, many of the individual papers in this special issue have additional protein identifications not included in the project-wide dataset(s).
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